Read a Prepared Annotation into Memory — prepare

Reads the Parquet tables of an annotation directory (or converts a GFF3/GTF file first, see prepare_isoformic_annotation()) and returns them as a list of tibbles. This is the table-based counterpart of the annot_data_*() accessors of IsoformicExperiment.

Usage

prepare_annotation(
  file_path,
  file_type = c("auto", "gff", "gtf"),
  output_path = NULL
)

Arguments

file_path: Path to an annotation directory or to a GFF3/GTF file.
file_type: Passed to prepare_isoformic_annotation() when file_path is a file.
output_path: Passed to prepare_isoformic_annotation().

Value

A named list with tibbles genes, transcripts, exons, seq_regions and a named list metadata.

Examples

gff <- system.file("extdata", "example.gff3", package = "isoformic")
annot <- prepare_annotation(gff, output_path = tempdir())
#> ℹ Using cached annotation directory /tmp/RtmpV2WK1u/example.
names(annot)
#> [1] "genes"       "transcripts" "exons"       "seq_regions" "metadata"   
head(annot$genes)
#> # A tibble: 3 × 14
#>   gene_id   gene_name gene_type source_gene_id gene_class gene_category dhs_type
#>   <chr>     <chr>     <chr>     <chr>          <chr>      <chr>         <chr>   
#> 1 ENSG0000… FLT1      protein_… NA             NA         NA            NA      
#> 2 ENSG0000… RBPJ      protein_… NA             NA         NA            NA      
#> 3 ENSG0000… PNCK      protein_… NA             NA         NA            NA      
#> # ℹ 7 more variables: coding_status <chr>, cumulative_support <chr>,
#> #   haplotype <chr>, seqid <chr>, start_pos <int>, end_pos <int>, strand <chr>